Revision: 20159
http://sourceforge.net/p/jmol/code/20159
Author: hansonr
Date: 2014-12-09 13:05:53 +0000 (Tue, 09 Dec 2014)
Log Message:
-----------
Jmol.___JmolVersion="14.3.11_2014.12.09"
bug fix: array.add("\t",array) broken 2014.12.04
bug fix: array.split("",true) doesn't handle CSV with new lines in quotes
Modified Paths:
--------------
trunk/Jmol/src/javajs/util/PT.java
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/javajs/util/PT.java
===================================================================
--- trunk/Jmol/src/javajs/util/PT.java 2014-12-05 04:21:46 UTC (rev 20158)
+++ trunk/Jmol/src/javajs/util/PT.java 2014-12-09 13:05:53 UTC (rev 20159)
@@ -573,6 +573,7 @@
*
* @param line
* @param next int[2] filled with [ptrQuote1, ptrAfterQuote2]
+ * next[1] will be -1 if unmatched quotes are found (continuation
on next line)
* @return unescaped string or null
*/
public static String getCSVString(String line, int[] next) {
@@ -590,8 +591,10 @@
haveEscape = true;
i++;
}
- if (i >= len)
+ if (i >= len) {
+ next[1] = -1;
return null; // unmatched
+ }
next[1] = i + 1;
String s = line.substring(pt + 1, i);
return (haveEscape ? rep(rep(s, "\"\"", "\0"), "\0","\"") : s);
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2014-12-05 04:21:46 UTC
(rev 20158)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2014-12-09 13:05:53 UTC
(rev 20159)
@@ -5028,6 +5028,8 @@
}
boolean isPlay = false;
boolean isRange = false;
+ String propName = null;
+ Object prop = null;
boolean isAll = false;
boolean isHyphen = false;
int[] frameList = new int[] { -1, -1 };
@@ -5105,6 +5107,11 @@
case T.range:
isRange = true;
break;
+ case T.property:
+ propName = stringParameter(3);
+ prop = (isArrayParameter(4) ? stringParameterSet(4) : paramAsStr(4));
+ i = slen;
+ break;
default:
frameControl(offset);
return;
@@ -5131,6 +5138,7 @@
frameList[i] %= 1000000;
int modelIndex = vwr.ms.getModelNumberIndex(frameList[0], useModelNumber,
false);
+
int modelIndex2 = -1;
if (haveFileSet && modelIndex < 0 && frameList[0] != 0) {
// may have frame 2.0 or frame 2 meaning the range of models in file 2
@@ -5166,6 +5174,11 @@
}
}
+ if (propName != null) {
+ if (modelIndex < 0)
+ return;
+ vwr.ms.setInfo(modelIndex, propName, prop);
+ }
if (!isPlay && !isRange || modelIndex >= 0)
vwr.setCurrentModelIndexClear(modelIndex, false);
if (isPlay && nFrames == 2 || isRange || isHyphen) {
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2014-12-05 04:21:46 UTC
(rev 20158)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2014-12-09 13:05:53 UTC
(rev 20159)
@@ -96,8 +96,6 @@
protected T[] st;
protected int slen;
- private Object[] lastData;
-
final static int ERROR_invalidArgument = 22;
public CmdExt() {
@@ -1619,7 +1617,7 @@
dataString.trim());
return;
}
- Object[] d = lastData = new Object[4];
+ Object[] d = new Object[4];
// not saving this data in the state?
if (dataType.equals("element_vdw")) {
// vdw for now
@@ -3600,7 +3598,6 @@
}
break;
case T.symop:
- String type;
int iop = 0;
P3 pt1 = null,
pt2 = null;
@@ -3611,7 +3608,7 @@
// show symop 3 "fmatrix"
iop = (tokAt(2) == T.integer ? intParameter(2) : 0);
}
- type = (tokAt(eval.iToken + 1) == T.string ?
stringParameter(++eval.iToken)
+ String type = (tokAt(eval.iToken + 1) == T.string ?
stringParameter(++eval.iToken)
: null);
checkLength(len = ++eval.iToken);
if (!chk)
@@ -3826,9 +3823,9 @@
msg = vwr.stm.getSavedStructure(shape);
break;
case T.data:
- type = ((len = slen) == 3 ? paramAsStr(2) : null);
+ String dtype = ((len = slen) == 3 ? paramAsStr(2) : null);
if (!chk) {
- Object[] data = (type == null ? this.lastData : vwr.getData(type));
+ Object[] data = vwr.getData(dtype);
msg = (data == null ? "no data" : Escape.encapsulateData(
(String) data[0], data[1], ((Integer) data[3]).intValue()));
}
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2014-12-05 04:21:46 UTC
(rev 20158)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2014-12-09 13:05:53 UTC
(rev 20159)
@@ -153,7 +153,7 @@
return evaluateFind(mp, args);
case T.format:
case T.label:
- return evaluateFormat(mp, op.intValue, args, tok == T.format);
+ return evaluateFormat(mp, op.intValue, args, tok == T.label);
case T.function:
return evaluateUserFunction(mp, (String) op.value, args, op.intValue,
op.tok == T.propselector);
@@ -1122,19 +1122,27 @@
asArray));
}
- /**
- * array.add(x) array.add(sep, x) array.sub(x) array.mul(x) array.mul3(x)
- * array.div(x) array.push() array.pop() array.split("")
- * array.split("\t",true)
- *
- * @param mp
- * @param tok
- * @param args
- * @return T/F
- * @throws ScriptException
- */
private boolean evaluateList(ScriptMathProcessor mp, int tok, SV[] args)
throws ScriptException {
+ // array.add(x)
+ // array.add(sep, x)
+ // array.sub(x)
+ // array.mul(x)
+ // array.mul3(x)
+ // array.div(x)
+ // array.push()
+ // array.pop()
+
+ // array.join()
+ // array.join(sep)
+ // array.join(sep,true)
+ // array.join("",true) (CSV)
+
+ // array.split()
+ // array.split(sep)
+ // array.split("\t",true)
+ // array.split("",true) (CSV)
+
int len = args.length;
SV x1 = mp.getX();
boolean isArray1 = (x1.tok == T.varray);
@@ -1160,94 +1168,103 @@
String[] sList1 = null, sList2 = null, sList3 = null;
if (len == 2) {
- // [...].add("\t", [...])
- // [...].split("\t", true) [split individual elements as strings]
- // [...].split("", true) [CSV split]
- // [...][...].join("x", true) [2D-array line join]
- // [...][...].join("", true) [CSV join]
- int itab = (args[0].tok == T.string ? 0 : 1);
- String tab = SV.sValue(args[itab]);
- if (len == 2) {
- Lst<SV> l = x1.getList();
- boolean isCSV = (tab.length() == 0);
- if (isCSV)
- tab = ",";
- if (tok == T.join) {
- SV[] s2 = new SV[l.size()];
- for (int i = l.size(); --i >= 0;) {
- Lst<SV> a = l.get(i).getList();
- if (a == null)
- s2[i] = l.get(i);
- else {
- SB sb = new SB();
- for (int j = 0, n = a.size(); j < n; j++) {
- if (j > 0)
- sb.append(tab);
- SV sv = a.get(j);
- sb.append(isCSV && sv.tok == T.string ? "\"" + PT.rep(
- (String) sv.value, "\"", "\"\"") + "\""
- : "" + sv.asString());
- }
- s2[i] = SV.newS(sb.toString());
+ // special add, join, split
+ String tab = SV.sValue(args[0]);
+ x2 = args[1];
+ if (tok == T.add) {
+ // [...].add("\t", [...])
+ sList1 = (isArray1 ? SV.strListValue(x1) : PT
+ .split(SV.sValue(x1), "\n"));
+ sList2 = (x2.tok == T.varray ? SV.strListValue(x2) : PT.split(
+ SV.sValue(x2), "\n"));
+ sList3 = new String[len = Math.max(sList1.length, sList2.length)];
+ for (int i = 0; i < len; i++)
+ sList3[i] = (i >= sList1.length ? "" : sList1[i]) + tab
+ + (i >= sList2.length ? "" : sList2[i]);
+ return mp.addXAS(sList3);
+ }
+ if (x2.tok != T.on)
+ return false; // second parameter must be "true" for now.
+ Lst<SV> l = x1.getList();
+ boolean isCSV = (tab.length() == 0);
+ if (isCSV)
+ tab = ",";
+ if (tok == T.join) {
+ // [...][...].join(sep, true) [2D-array line join]
+ // [...][...].join("", true) [CSV join]
+ SV[] s2 = new SV[l.size()];
+ for (int i = l.size(); --i >= 0;) {
+ Lst<SV> a = l.get(i).getList();
+ if (a == null)
+ s2[i] = l.get(i);
+ else {
+ SB sb = new SB();
+ for (int j = 0, n = a.size(); j < n; j++) {
+ if (j > 0)
+ sb.append(tab);
+ SV sv = a.get(j);
+ sb.append(isCSV && sv.tok == T.string ? "\""
+ + PT.rep((String) sv.value, "\"", "\"\"") + "\"" : ""
+ + sv.asString());
}
+ s2[i] = SV.newS(sb.toString());
}
- return mp.addXAV(s2);
}
- SV[] sa = new SV[l.size()];
- if (isCSV)
- tab = "\0";
- int[] next = new int[2];
- for (int i = l.size(); --i >= 0;) {
- String line = l.get(i).asString();
- if (isCSV) {
- next[1] = 0;
- next[0] = 0;
- int last = 0;
- while (true) {
- String s = PT.getCSVString(line, next);
- if (s == null) {
- line = line.substring(0, last)
- + line.substring(last).replace(',', '\0');
- break;
+ return mp.addXAV(s2);
+ }
+ // [...].split(sep, true) [split individual elements as strings]
+ // [...].split("", true) [CSV split]
+ Lst<SV> sa = new Lst<SV>();
+ if (isCSV)
+ tab = "\0";
+ int[] next = new int[2];
+ for (int i = 0, nl = l.size(); i < nl; i++) {
+ String line = l.get(i).asString();
+ if (isCSV) {
+ next[1] = 0;
+ next[0] = 0;
+ int last = 0;
+ while (true) {
+ String s = PT.getCSVString(line, next);
+ if (s == null) {
+ if (next[1] == -1) {
+ // unmatched -- continue with next line if present
+ // or just close quotes gracefully
+ line += (++i < nl ? "\n" + l.get(i).asString() : "\"");
+ next[1] = last;
+ continue;
}
line = line.substring(0, last)
- + line.substring(last, next[0]).replace(',', '\0') + s
- + line.substring(next[1]);
- next[1] = last = next[0] + s.length();
+ + line.substring(last).replace(',', '\0');
+ break;
}
+ line = line.substring(0, last)
+ + line.substring(last, next[0]).replace(',', '\0') + s
+ + line.substring(next[1]);
+ next[1] = last = next[0] + s.length();
}
- String[] linaa = line.split(tab);
- Lst<SV> la = new Lst<SV>();
- for (int j = 0, n = linaa.length; j < n; j++) {
- String s = linaa[j];
- if (s.indexOf(".") < 0)
- try {
- la.addLast(SV.newI(Integer.parseInt(s)));
- continue;
- } catch (Exception e) {
- }
- else
- try {
- la.addLast(SV.getVariable(Float.valueOf(Float.parseFloat(s))));
- continue;
- } catch (Exception ee) {
- }
- la.addLast(SV.newS(s));
- }
- sa[i] = SV.getVariableList(la);
}
- return mp.addXObj(SV.getVariable(sa));
+ String[] linaa = line.split(tab);
+ Lst<SV> la = new Lst<SV>();
+ for (int j = 0, n = linaa.length; j < n; j++) {
+ String s = linaa[j];
+ if (s.indexOf(".") < 0)
+ try {
+ la.addLast(SV.newI(Integer.parseInt(s)));
+ continue;
+ } catch (Exception e) {
+ }
+ else
+ try {
+ la.addLast(SV.getVariable(Float.valueOf(Float.parseFloat(s))));
+ continue;
+ } catch (Exception ee) {
+ }
+ la.addLast(SV.newS(s));
+ }
+ sa.addLast(SV.getVariableList(la));
}
-
- sList1 = (isArray1 ? SV.strListValue(x1) : PT.split(SV.sValue(x1),
"\n"));
- x2 = args[1 - itab];
- sList2 = (x2.tok == T.varray ? SV.strListValue(x2) : PT.split(
- SV.sValue(x2), "\n"));
- sList3 = new String[len = Math.max(sList1.length, sList2.length)];
- for (int i = 0; i < len; i++)
- sList3[i] = (i >= sList1.length ? "" : sList1[i]) + tab
- + (i >= sList2.length ? "" : sList2[i]);
- return mp.addXAS(sList3);
+ return mp.addXObj(SV.getVariableList(sa));
}
x2 = (len == 0 ? SV.newV(T.all, "all") : args[0]);
boolean isAll = (x2.tok == T.all);
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-12-05 04:21:46 UTC
(rev 20158)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-12-09 13:05:53 UTC
(rev 20159)
@@ -15,8 +15,31 @@
TODO: design and implement sidechain mutation -- MUTATE command ?
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
-Jmol.___JmolVersion="14.3.11_2014.12.04"
+Jmol.___JmolVersion="14.3.11_2014.12.09"
+
+bug fix: array.add("\t",array) broken 2014.12.04
+bug fix: array.split("",true) doesn't handle CSV with new lines in quotes
+
+JmolVersion="14.3.11_2014.12.06"
+
+new feature: MODEL 1 PROPERTY "xxx" @x
+ -- adds property to model's auxilliaryInfo
+ -- if x is an array, then these become atom data accessible via %{...}
+ -- for example:
+ x = "1\n2\n3\n".lines
+ model 1 property "mydata" @x
+ {model=1}.property_n = {*}.label("%{mydata}") // converts to numbers
+
+ data "myd @x" // similar, but not model-based
+ label %{myd}
+
+
+bug fix: format() function broken
+bug fix: SHOW DATA should be cleared when a file is loaded
+
+JmolVersion="14.3.11_2014.12.04"
+
new feature: "....".split("",true) // CSV split of string to array of arrays
new feature: [...].split("",true) // CSV split of array to array of arrays
new feature: "...".split("\t",true) // tab split of string to array of arrays
@@ -33,7 +56,7 @@
x = load("test.csv").split("",true).col(3) //3rd column from CSV
-Jmol.___JmolVersion="14.3.11_2014.12.02"
+JmolVersion="14.3.11_2014.12.02"
bug fix: for (x in yUpperCase) fails
bug fix: draw SYMOP fails for incommensurate space groups
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2014-12-05 04:21:46 UTC (rev
20158)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2014-12-09 13:05:53 UTC (rev
20159)
@@ -2685,6 +2685,7 @@
chainList.clear();
cm.clear();
definedAtomSets.clear();
+ lastData = null;
if (dm != null)
dm.clear();
setBooleanProperty("legacyjavafloat", false);
@@ -3208,15 +3209,17 @@
cm.setPropertyColorRangeData(data, bs);
}
+ private Object[] lastData;
+
public void setData(String type, Object[] data, int arrayCount,
int matchField, int matchFieldColumnCount, int field,
int fieldColumnCount) {
- getDataManager().setData(type, data, arrayCount, getAtomCount(),
matchField,
+ getDataManager().setData(type, lastData = data, arrayCount,
getAtomCount(), matchField,
matchFieldColumnCount, field, fieldColumnCount);
}
public Object[] getData(String type) {
- return getDataManager().getData(type);
+ return (type == null ? lastData : getDataManager().getData(type));
}
public float[] getDataFloat(String label) {
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